Based on magnetotelluric (MT) array data, we have obtained the first three‐dimensional (3‐D) electrical resistivity model at the Gaoligong intracontinental block boundary in southeastern Tibetan Plateau where the Quaternary intraplate Tengchong volcanism and seismic activities occur. Comparing with results of previous geophysical studies in the area, our MT model clearly reveals three conductive bodies in the depth ranges of 10–30 km in the Tengchong volcano area, which we interpret as three middle‐lower crustal magma chambers associated with the Tengchong volcanism. Seismogenic faults in the Gaoligong Shear Zone (GLGSZ) are characterized by subvertical conductive zones bounded by resistive upper crustal layer on both sides. Earthquakes of moderate magnitudes near the GLGSZ have all occurred within the conductive fault zones at the bottom of the upper resistive crust. More importantly, one large resistive body was imaged at middle‐lower crustal depth beneath the GLGSZ, which seems to block the previously proposed horizontal crustal channel flow along this intracontinental block boundary. Our 3‐D model indicates that crustal channel flow could take place east of the GLGSZ. The current study provides evidence from electrical resistivity structure for the middle‐lower crustal magma chambers in the Tengchong volcano area and detailed 3‐D electrical structure of crustal channel flow in this active tectonic region.